R Notebook

library(Seurat)
library(monocle)
library(cowplot)
wolfrum.predicted_labels <- readRDS('output/seurat_objects/wolfrum/wolfrum.predicted_labels_180831.rds')

Monocle wolfrum preadipocytes

Ran Monocle on the Wolfrum subset with the same gene list that was used to build the 180831 trajectory.

predictions <- wolfrum.predicted_labels@meta.data['predictions_pca.predicted.id']

Error: object 'wolfrum.predicted_labels' not found

  rownames(df) <- states

Error in `.rowNamesDF<-`(x, value = value) : 
  missing values in 'row.names' are not allowed

states.prediction

     n Progenitor Metabolic  ECM
4 1158       0.00      1.00 0.00
1 1254       0.11      0.21 0.69
5  170       0.00      1.00 0.00
2  207       0.05      0.91 0.04
3    5       0.00      1.00 0.00

states.prediction

              n   4    1    5    2 3
Progenitor 2924 0.0 0.05 0.00 0.00 0
Metabolic  5740 0.2 0.05 0.03 0.03 0
ECM         869 0.0 0.99 0.00 0.01 0

Monocle wolfrum preadipocytes integrated 180831